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At least 19 records

Towards the Interoperability of Web, Database, and Mass Storage Technologies for Petabyte Archives

At the San Diego Supercomputer Center, a massive data analysis system (MDAS) is being developed to support data-intensive applications that manipulate terabyte sized data sets. The objective is to support scientific application access to data whether it is located at a Web site, stored as an object in a database, and/or storage in an archival storage system. We are developing a suite of demonstration programs which illustrate how Web, database (DBMS), and archival storage (mass storage) technologies can be integrated. An application presentation interface is being designed that integrates data access to all of these sources. We have developed a data movement interface between the Illustra object-relational database and the NSL UniTree archival storage system running in a production mode at the San Diego Supercomputer Center. With this interface, an Illustra client can transparently access data on UniTree under the control of the Illustr DBMS server. The current implementation is based on the creation of a new DBMS storage manager class, and a set of library functions that allow the manipulation and migration of data stored as Illustra 'large objects'. We have extended this interface to allow a Web client application to control data movement between its local disk, the Web server, the DBMS Illustra server, and the UniTree mass storage environment. This paper describes some of the current approaches successfully integrating these technologies. This framework is measured against a representative sample of environmental data extracted from the San Diego Ba Environmental Data Repository. Practical lessons are drawn and critical research areas are highlighted.

Moore, Reagan

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases.

Kulkarni, Deepak

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases. To appear in an article of Journal of Database Management.

Kulkarni, Deepak

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

59 BASIC BIOLOGICAL SCIENCES

Access to Space: Providing a Ride to Your Future

This viewgraph presentation gives an overview of the Access to Space website, including information on the personnel structure, mission statement, process flow, project formulation, project support, web-based tools and database, web site contents, implementation plan, user registration, mission data input, capabilities of the website, and accomplishments thus far.

Cutlip, William E.

Ground Support Software for Spaceborne Instrumentation

ION is a system of ground support software for the ion and neutral mass spectrometer (INMS) instrument aboard the Cassini spacecraft. By incorporating commercial off-the-shelf database, Web server, and Java application components, ION offers considerably more ground-support-service capability than was available previously. A member of the team that operates the INMS or a scientist who uses the data collected by the INMS can gain access to most of the services provided by ION via a standard pointand click hyperlink interface generated by almost any Web-browser program running in almost any operating system on almost any computer. Data are stored in one central location in a relational database in a non-proprietary format, are accessible in many combinations and formats, and can be combined with data from other instruments and spacecraft. The use of the Java programming language as a system-interface language offers numerous capabilities for object-oriented programming and for making the database accessible to participants using a variety of computer hardware and software.

Anicich, Vincent

Augmented Reality Technologies for Radiation Safety Training: A Systematic Review of Sensor Integration and Visualization Approaches

This paper presents a comprehensive systematic review examining the application of augmented reality (AR) and sensor technologies for visualizing ionizing radiation in virtual training environments. The review methodology involved systematic identification and analysis of the relevant literature based on predetermined criteria including publication type, year of publication, application domain, and technological approach. The literature search encompassed publications from 2011 to 2021 across four major academic databases: Web of Science, Google Scholar, IEEE Xplore, and Scopus. Through rigorous screening following PRISMA 2020 guidelines, 23 research articles met the inclusion criteria for detailed analysis. From 404 initial database records, 360 were excluded during title/abstract screening (primarily for lacking AR components, radiation focus, or training applications) and 4 during full-text assessment (all for lacking sensor integration). The findings reveal that AR-based ionizing radiation visualization has been successfully implemented across diverse domains, including nuclear facility operations, medical procedures, CERN research activities, and educational and monitoring applications. The analysis identified multiple dimensions of impact, encompassing distinct benefits, emerging opportunities, and implementation challenges associated with AR deployment for ionizing radiation training. Each of these dimensions is comprehensively examined and documented within this review. Additionally, this study identifies critical research gaps that currently limit the full potential of AR technology in supporting ionizing radiation training programs. These gaps are systematically analyzed and discussed to establish clear directions for future research endeavors in this emerging field.

61 - RADIATION PROTECTION AND DOSIMETRY

Characterizing Nearby Stars: Age and Activity

The funds in this grant were used to support costs for observing and data analysis over the past two years. During this time I have been obtaining low-resolution (R-2,000) spectra for about 5,000 solar-type stars (late-F and G dwarfs) that are within 60 parsecs of the Sun. The sample was defined with results from the Hipparcos mission, and the spectra were obtained at Kitt Peak National Observatory, using the Coude Feed telescope, and at Cerro Tololo Interamerican Observatory, using their 1.5 m telescopes for stars below -40 declination. Nearly all the observed spectra have been reduced and analyzed. What is determined is R-prime, an index of the chromospheric emission in the cores of the Ca II H and K lines relative to the nearby continuum, and normalized for the color of the star. Chromospheric emission arises from magnetic activity on the star, and that is turn is driven by rotation. Solar-type stars spin down as they age, and so they get weaker in their chromospheric emission as well. Thus this R-prime index can be used to estimate the ages of stars. A few stars remain to be observed at Kitt Peak, and follow-up high-resolution spectra are being obtained of the most active stars seen, but the majority of the starting sample have been completed. The spectra obtained are also being analyzed to yield an index of overall metallicity for each star, and this will be used to study Galactic evolution questions. These metallicities will form the first large dataset of high and consistent quality. Initial results from this work have been used to define targets for a SIRTF Legacy program, for stars to study for planetary transits, and for SETI efforts. Because of the large number of stars involved, most of the data will be made available on the web, although some specific papers about the results are in preparation. The web database is being constructed.

Soderblom, David

The Burst and Transient Source Experiment (BATSE) Earth Occultation Catalog

The hard X-ray sky was continuously monitored with the BATSE experiment on the Compton Gamma Ray observatory using the Earth Occultation method. Known sources were monitored twice every orbit and transients could be detected at about the approx. 50 mCrab level on a daily basis. I will summarize the results from our catalog of 179 monitored sources, highlighting observations of black holes and energy spectra for the 83 firmly detected sources and FITS files for all 179 sources. This web database can serve as a guide and comparison tool for future observations with EXIST.

Wilson-Hodge, Colleen A.

Web-accessible sorption database (Interim Progress Report)

This progress report (Level 4 Milestone Number M4SF-26LL010204053) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Crystalline Host Rock Properties & Processes - LLNL Number SF-26LL01020405. This research is focused on the development of a web-accessible database of sorption data for minerals and rocks (bentonite backfill and crystalline host rock) that are likely to be present in a US hosted repository, including elevated temperature data that are expected in a DPC DGR scenario.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

A new database website for nuclear level densities

We introduce a new open-access, web-based database (http://nld.ascsn.net), Current Archive of Nuclear Density of Levels (CANDL), that hosts experimental nuclear level density (NLD) datasets from a variety of techniques and energy ranges. Built using the Dash framework in Python, the database is designed to be interactive and user-friendly, allowing researchers to search, visualize, fit, and export NLD data with minimal effort. This resource includes data extracted from evaporation spectra, Oslo method variants, and other experimental techniques that cover excitation energies beyond the neutron resonance region. The database supports on-the-fly fitting with two widely-used phenomenological models—the Constant Temperature (CT) model and the Back-Shifted Fermi Gas (BSFG) model—selected for their simplicity and computational efficiency. Future versions aim to include additional datasets and model types, as well as easy-to-use interfaces to data science techniques. Here, this platform offers a vital tool for the nuclear physics, astrophysics, medicine, and reactor design communities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

DDD: Dynamic Database for Diatomics

We have developed as web-based database containing spectra of diatomic moiecuies. All data is computed from first principles, and if a user requests data for a molecule/ion that is not in the database, new calculations are automatically carried out on that species. Rotational, vibrational, and electronic transitions are included. Different levels of accuracy can be selected from qualitatively correct to the best calculations that can be carried out. The user can view and modify spectroscopic constants, view potential energy curves, download detailed high temperature linelists, or view synthetic spectra.

Schwenke, David

Web-Based Satellite Products Database for Meteorological and Climate Applications

The need for ready access to satellite data and associated physical parameters such as cloud properties has been steadily growing. Air traffic management, weather forecasters, energy producers, and weather and climate researchers among others can utilize more satellite information than in the past. Thus, it is essential that such data are made available in near real-time and as archival products in an easy-access and user friendly environment. A host of Internet web sites currently provide a variety of satellite products for various applications. Each site has a unique contribution with appeal to a particular segment of the public and scientific community. This is no less true for the NASA Langley's Clouds and Radiation (NLCR) website (http://www-pm.larc.nasa.gov) that has been evolving over the past 10 years to support a variety of research projects This website was originally developed to display cloud products derived from the Geostationary Operational Environmental Satellite (GOES) over the Southern Great Plains for the Atmospheric Radiation Measurement (ARM) Program. It has evolved into a site providing a comprehensive database of near real-time and historical satellite products used for meteorological, aviation, and climate studies. To encourage the user community to take advantage of the site, this paper summarizes the various products and projects supported by the website and discusses future options for new datasets.

Phan, Dung

Web interfaces to relational databases

This reports on a project to extend the capabilities of a Virtual Research Center (VRC) for NASA's Advanced Concepts Office. The work was performed as part of NASA's 1995 Summer Faculty Fellowship program and involved the development of a prototype component of the VRC - a database system that provides data creation and access services within a room of the VRC. In support of VRC development, NASA has assembled a laboratory containing the variety of equipment expected to be used by scientists within the VRC. This laboratory consists of the major hardware platforms, SUN, Intel, and Motorola processors and their most common operating systems UNIX, Windows NT, Windows for Workgroups, and Macintosh. The SPARC 20 runs SUN Solaris 2.4, an Intel Pentium runs Windows NT and is installed on a different network from the other machines in the laboratory, a Pentium PC runs Windows for Workgroups, two Intel 386 machines run Windows 3.1, and finally, a PowerMacintosh and a Macintosh IIsi run MacOS.

Carlisle, W. H.

Querying Semi-Structured Data

The amount of data of all kinds available electronically has increased dramatically in recent years. The data resides in different forms, ranging from unstructured data in the systems to highly structured in relational database systems. Data is accessible through a variety of interfaces including Web browsers, database query languages, application-specic interfaces, or data exchange formats. Some of this data is raw data, e.g., images or sound. Some of it has structure even if the structure is often implicit, and not as rigid or regular as that found in standard database systems. Sometimes the structure exists but has to be extracted from the data. Sometimes also it exists but we prefer to ignore it for certain purposes such as browsing. We call here semi-structured data this data that is (from a particular viewpoint) neither raw data nor strictly typed, i.e., not table-oriented as in a relational model or sorted-graph as in object databases. As will seen later when the notion of semi-structured data is more precisely de ned, the need for semi-structured data arises naturally in the context of data integration, even when the data sources are themselves well-structured. Although data integration is an old topic, the need to integrate a wider variety of data- formats (e.g., SGML or ASN.1 data) and data found on the Web has brought the topic of semi-structured data to the forefront of research. The main purpose of the paper is to isolate the essential aspects of semi- structured data. We also survey some proposals of models and query languages for semi-structured data. In particular, we consider recent works at Stanford U. and U. Penn on semi-structured data. In both cases, the motivation is found in the integration of heterogeneous data.

DATA MANAGEMENT

Spectroscopic data for an astronomy database

Very few of the atomic and molecular data used in analyses of astronomical spectra are currently available in World Wide Web (WWW) databases that are searchable with hypertext browsers. We have begun to rectify this situation by making extensive atomic data files available with simple search procedures. We have also established links to other on-line atomic and molecular databases. All can be accessed from our database homepage with URL: http:// cfa-www.harvard.edu/ amp/ data/ amdata.html.

Parkinson, W. H.

Web Exploration Tools for a Fast Federated Optical Survey Database

We implemented several new web-based tools to improve the efficiency and versatility of access to the APS Catalog of the POSS I (Palomar Observatory-National Geographic Sky Survey) and its associated image database. The most important addition was a federated database system to link the APS Catalog and image database into one Internet-accessible database. With the FDBS, the queries and transactions on the integrated database are performed as if it were a single database. We installed Myriad the FDBS developed by Professor Jaideep Srivastava and members of his group in the University of Minnesota Computer Science Department. It is the first system to provide schema integration, query processing and optimization, and transaction management capabilities in a single framework. The attached figure illustrates the Myriad architecture. The FDBS permits horizontal access to the data, not just vertical. For example, for the APS, queries can be made not only by sky position, but also by any parameter present in either of the databases. APS users will be able to produce an image of all the blue galaxies and stellar sources for comparison with x-ray source error ellipses from AXAF (X Ray Astrophysics Facility) (Chandra) for example. The FDBS is now available as a beta release with the appropriate query forms at our web site. While much of our time was occupied with adapting Myriad to the APS environment, we also made major changes in Star Base, our DBMS for the Catalog, at the web interface to improve its efficiency for issuing and processing queries. Star Base is now three times faster for large queries. Improvements were also made at the web end of the image database for faster access; although work still needs to be done to the image database itself for more efficient return with the FDBS. During the past few years, we made several improvements to the database pipeline that creates the individual plate databases queries by StarBase. The changes include improved positions especially for galaxies, using a new median centroider and integrated magnitudes for galaxies with an improved density-to-intensity calibration with a "sky" background subtraction. In the original version of StarBase the object classification fainter than 19.5-20.0 mag., was an extrapolation of the networks trained on brighter objects. We have used a new catalog of galaxies at the NGP to train a neural network on objects fainter than 20th mag. This improved classification is used in the new version of StarBase. We have also added a FITS table option for the returned data from queries on the object catalog. The APS image database includes images in both colors so we have added a tool for querying the image database in both colors simultaneously. The images can be displayed in parallel or blinked for comparison.

Humphreys, Roberta M.

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing